Using data from Earth Microbiome Project

General Discussion
1

Hi all,

I have some general questions about using data linked to the Earth Microbiome Project (EMP).
I will type my concerns and the questions in a list below

  1. I wanted to download some 16S sequenced data from Qiita linked to EMP. I wanted use the EBI-ENA accession number provided in qiita database to download the same data set from the European nucleotide archive (ENA). I want to know if I can access the same data set that is available under a particular qiita-id using the EBI accession that is provided?
    I'm asking this because I found that for some projects, the description in ENA is for 18S data sequencing while the 'data type' indicated in qiita database is 16S.

  2. Does anyone have any experience using EMP DNA extraction protocol for liquid material?
    The protocol that is available in the EMP website (Earth Microbiome Project (EMP) high throughput (HTP) DNA extraction protocol) says to use 250uL of liquid material for DNA extraction. I was wondering if that amount is enough to capture all the microbes represented in a particular sample. Moreover, isn't filtration through a particular pore size (e.g- 0.22um) required to concentrate the microbes for DNA extraction?

Sorry for the long message. Would be grateful to know what you all think about this.

Any help is much appreciated.

Many thanks in advance!

Uthpala

2

Hi @uth,

I am not sure — I am seeing if @antgonza can help.

@Luke_Thompson is the lead author and may be able to help.

Thank you all!

1 Like
3

Thank you so much for the prompt reply. I hope @Luke_Thompson and @antgonza might be able to help with this! waiting for their reply :grinning:

Thank s again!

Uthpala

4

Just adding here for completeness.

If the rawest data was initially submitted to Qiita and then deposited to EBI-ENA your will find the same raw data in both places. However, metadata in Qiita is updated based on requirements for meta-analysis or standards (like MIMARKS); in other words, you will find a more detailed metadata for both sample and preparations in Qiita.

Now, in specific, @uth, who contacted the qiita.help@gmail.com account, was wondering about accession ERP020508. This set of samples where originally processed for 18S and published; after this the samples were sent to the EMP for 16S processing and these are the samples/preparations that are in both Qiita and EBI-ENA. Thus, the 16S/18S confusion.

2 Likes
5

Thank you for your clarification, again. I solved this by contacting qiita.help@gmail.com.

Thanks
Uth